RE: Vanishing bonds in small molecule during psf generation.

From: Christian Blouin (
Date: Wed Jul 18 2007 - 14:13:33 CDT


The problem at the time was indeed embarrassing oversight/typos. Thank you
very much for the helping hand! I now have to deal with the fact that many
of the bonds that I've specified aren't parameterized in the par_all27*
file. Also, for some reasons, atoms are added during psfgen which I suspect
is an attempt to cap the polypeptide chain (even if there are none).


Getting a cofactor up and running feels like a dark art! Is everyone
modeling proteins with cofactors end-up with their own _handcrafted_ top and
par files?




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